Render queue, more layers?
Can you not assign different materials to the different particle systems (Mat 1 and Mat 2) each with a Pass ID, and then assign an Object ID (Letter A, Letter B, etc) to each geometry mesh, and then do one render and separate everything in Compositing? You could then pipe each combination into a File Output node OR you could render to MultiLayer EXR frame files and handle the layer separations in After Effects.